Technical Abstract:
Alfalfa plants have somewhere between 35,000 and 45,000 genes within their 32 chromosomes. Until recently, only one to a few expressed genes in alfalfa could be studied at a single time. This technological limitation has severely hampered our ability to identify the genes needed for alfalfa improvement. A major step forward for measuring the activity of expressed genes occurred in the development of GeneChips, born of technology bringing together DNA and semiconductor research. In September 2005, a Medicago GeneChip was released by Affymetrix, the company specializing in development and manufacturing of GeneChips. The Medicago GeneChip includes probe sets for genes of three different organisms. The majority of the genes (about 52,700 probe sets) are from barrel medic (Medicago truncatula), an annual forage species grown widely in Australia, which is closely related to alfalfa (M. sativa). In addition, there are probe sets for approximately 1,800 genes from alfalfa, and probe sets all of the genes from the bacterium Sinorhizobium meliloti, which is the microsymbiont that nodulates alfalfa for fixing nitrogen. At the DNA sequence identity level, genes in barrel medic and alfalfa are approximately 95% identical. The question is whether or not the Medicago GeneChip can be used to identify expressed genes in alfalfa. The assumption is that the barrel medic probe sets on the GeneChip should detect the majority of expressed alfalfa genes. We set out to test this assumption by analyzing the expression of genes in leaves and roots of 14-day-old seedlings of alfalfa and barrel medic. Approximately 24,371 - 28,668 probes on the GeneChip were active in barrel medic root and leaf tissues. On the other hand 21,526 - 23,202 probes were active in alfalfa root and leaf samples. This was good news for alfalfa research, as the GeneChip was found to be applicable for the expression of thousands of genes that can lead to the discovery of agronomically important genes in alfalfa. This new Medicago genomics research tool will be of great utility for the discovery and characterization of genes for improving stand persistence, forage quality, pest and disease resistance, and other traits needed for increased economic vitality of alfalfa and environmentally friendly agricultural production.